Training alignment parameters for arbitrary sequencers with LAST-TRAIN

SUMMARY: LAST-TRAIN improves sequence alignment accuracy by inferring substitution and gap scores that fit the frequencies of substitutions, insertions, and deletions in a given dataset. We have applied it to mapping DNA reads from IonTorrent and PacBio RS, and we show that it reduces reference bias...

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Detalles Bibliográficos
Autores principales: Hamada, Michiaki, Ono, Yukiteru, Asai, Kiyoshi, Frith, Martin C
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2017
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5351549/
https://www.ncbi.nlm.nih.gov/pubmed/28039163
http://dx.doi.org/10.1093/bioinformatics/btw742
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author Hamada, Michiaki
Ono, Yukiteru
Asai, Kiyoshi
Frith, Martin C
author_facet Hamada, Michiaki
Ono, Yukiteru
Asai, Kiyoshi
Frith, Martin C
author_sort Hamada, Michiaki
collection PubMed
description SUMMARY: LAST-TRAIN improves sequence alignment accuracy by inferring substitution and gap scores that fit the frequencies of substitutions, insertions, and deletions in a given dataset. We have applied it to mapping DNA reads from IonTorrent and PacBio RS, and we show that it reduces reference bias for Oxford Nanopore reads. AVAILABILITY AND IMPLEMENTATION: the source code is freely available at http://last.cbrc.jp/ SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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spelling pubmed-53515492017-03-21 Training alignment parameters for arbitrary sequencers with LAST-TRAIN Hamada, Michiaki Ono, Yukiteru Asai, Kiyoshi Frith, Martin C Bioinformatics Applications Notes SUMMARY: LAST-TRAIN improves sequence alignment accuracy by inferring substitution and gap scores that fit the frequencies of substitutions, insertions, and deletions in a given dataset. We have applied it to mapping DNA reads from IonTorrent and PacBio RS, and we show that it reduces reference bias for Oxford Nanopore reads. AVAILABILITY AND IMPLEMENTATION: the source code is freely available at http://last.cbrc.jp/ SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2017-03-15 2016-11-23 /pmc/articles/PMC5351549/ /pubmed/28039163 http://dx.doi.org/10.1093/bioinformatics/btw742 Text en © The Author 2016. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Applications Notes
Hamada, Michiaki
Ono, Yukiteru
Asai, Kiyoshi
Frith, Martin C
Training alignment parameters for arbitrary sequencers with LAST-TRAIN
title Training alignment parameters for arbitrary sequencers with LAST-TRAIN
title_full Training alignment parameters for arbitrary sequencers with LAST-TRAIN
title_fullStr Training alignment parameters for arbitrary sequencers with LAST-TRAIN
title_full_unstemmed Training alignment parameters for arbitrary sequencers with LAST-TRAIN
title_short Training alignment parameters for arbitrary sequencers with LAST-TRAIN
title_sort training alignment parameters for arbitrary sequencers with last-train
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5351549/
https://www.ncbi.nlm.nih.gov/pubmed/28039163
http://dx.doi.org/10.1093/bioinformatics/btw742
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AT onoyukiteru trainingalignmentparametersforarbitrarysequencerswithlasttrain
AT asaikiyoshi trainingalignmentparametersforarbitrarysequencerswithlasttrain
AT frithmartinc trainingalignmentparametersforarbitrarysequencerswithlasttrain

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